All of the spin comparison
functions display their results as points or lines in a
two-dimensional plot called a "Spin Sequence Comparison Plot" (
see section SPIN Sequence Comparison Plot).
Sets of matches from a single invocation of a
comparison command are termed "a result". Each result is plotted using
a single colour which can be configured via the results manager
(
see section Result manager).

At the right hand side is a set of square boxes with the
same colours as the dots drawn in the adjacent plot. These
icon-like objects represent individual results and allow the user to
operate on them. For example clicking with the right mouse button brings
up the pop-up menu beneath the "matching words"
result contains the results menu for this result
(
see section Result manager).
These icons can also be used to
drag and drop the results to which they correspond. This is activated by
pressing the middle mouse button, or Alt left mouse button,
over the box and then moving the cursor
over the Spin Sequence Comparison Plot to the new location or anywhere outside the Spin Sequence Comparison Plot
(
see section Drag and drop).

Crosshairs can be turned on or off using the check button labelled
"crosshairs". The x and y positions of the crosshairs are indicated in
the two boxes to the right of the check box.

Each sequence displayed in a Spin Sequence Comparison Plot will have a cursor
of a particular colour. In the picture above, the sequence on the horizontal
axis has a vertical blue cursor whereas the sequence on the vertical axis has
a horizontal olive green cursor. In general,
the same sequence displayed in several Spin Sequence Comparison Plots will have
a cursor of the same colour.
The user can move a cursor by clicking and dragging
with the middle mouse button, or with Alt left mouse button.
This will move all other
cursors displayed that relate to the sequence, whether they are in
different Spin Sequence Comparison Plots or within the sequence display.

Plots can be enlarged either by resizing the window or zooming. Zooming
is achieved by holding down the control key and right mouse button and
dragging out a rectangle. This process can be repeated.
The Back button will restore the plot to the previous magnification.

To illustrate further uses of the program we include some more screen
dumps below.

(Click for full size image)

The picture above shows the results after performing a "Find similar spans"
comparison between the three reading frames of two DNA sequences, producing
nine superimposed sets of results.

(Click for full size image)

Local alignment searches join similar segments with lines. The above
screen dump shows such an analysis in which
genomic DNA containing 7 exons and is compared to
its corresponding cDNA.

(Click for full size image)

The above screendump shows a global alignment of the same pair of
sequences.

This page is maintained by
staden-package.
Last generated on 22 October 2002.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/spin_unix_7.html